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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-49419382-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49419382&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49419382,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000273588.9",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*",
"transcript": "NM_000481.4",
"protein_id": "NP_000472.2",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 403,
"cds_start": 574,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "ENST00000273588.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*",
"transcript": "ENST00000273588.9",
"protein_id": "ENSP00000273588.3",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 403,
"cds_start": 574,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "NM_000481.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283189",
"gene_hgnc_id": null,
"hgvs_c": "c.811C>T",
"hgvs_p": "p.Gln271*",
"transcript": "ENST00000636166.1",
"protein_id": "ENSP00000490106.1",
"transcript_support_level": 5,
"aa_start": 271,
"aa_end": null,
"aa_length": 482,
"cds_start": 811,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 2266,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*",
"transcript": "ENST00000395338.7",
"protein_id": "ENSP00000378747.2",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 386,
"cds_start": 574,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 678,
"cdna_end": null,
"cdna_length": 1831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*",
"transcript": "NM_001164712.2",
"protein_id": "NP_001158184.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 386,
"cds_start": 574,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.493C>T",
"hgvs_p": "p.Gln165*",
"transcript": "ENST00000638063.1",
"protein_id": "ENSP00000489760.1",
"transcript_support_level": 5,
"aa_start": 165,
"aa_end": null,
"aa_length": 376,
"cds_start": 493,
"cds_end": null,
"cds_length": 1131,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 1783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.442C>T",
"hgvs_p": "p.Gln148*",
"transcript": "NM_001164710.2",
"protein_id": "NP_001158182.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 359,
"cds_start": 442,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 465,
"cdna_end": null,
"cdna_length": 1865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.442C>T",
"hgvs_p": "p.Gln148*",
"transcript": "ENST00000458307.6",
"protein_id": "ENSP00000415619.2",
"transcript_support_level": 2,
"aa_start": 148,
"aa_end": null,
"aa_length": 359,
"cds_start": 442,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.493C>T",
"hgvs_p": "p.Gln165*",
"transcript": "ENST00000635808.1",
"protein_id": "ENSP00000489620.1",
"transcript_support_level": 5,
"aa_start": 165,
"aa_end": null,
"aa_length": 359,
"cds_start": 493,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 516,
"cdna_end": null,
"cdna_length": 1610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Gln144*",
"transcript": "ENST00000538581.6",
"protein_id": "ENSP00000443200.2",
"transcript_support_level": 2,
"aa_start": 144,
"aa_end": null,
"aa_length": 355,
"cds_start": 430,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 2038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.418C>T",
"hgvs_p": "p.Gln140*",
"transcript": "ENST00000636865.1",
"protein_id": "ENSP00000490601.1",
"transcript_support_level": 5,
"aa_start": 140,
"aa_end": null,
"aa_length": 351,
"cds_start": 418,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*",
"transcript": "ENST00000637682.1",
"protein_id": "ENSP00000489856.1",
"transcript_support_level": 5,
"aa_start": 192,
"aa_end": null,
"aa_length": 351,
"cds_start": 574,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 581,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Gln136*",
"transcript": "NM_001164711.2",
"protein_id": "NP_001158183.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 347,
"cds_start": 406,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Gln136*",
"transcript": "ENST00000636522.1",
"protein_id": "ENSP00000489758.1",
"transcript_support_level": 2,
"aa_start": 136,
"aa_end": null,
"aa_length": 347,
"cds_start": 406,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 1620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Gln144*",
"transcript": "ENST00000427987.6",
"protein_id": "ENSP00000403821.2",
"transcript_support_level": 5,
"aa_start": 144,
"aa_end": null,
"aa_length": 338,
"cds_start": 430,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 568,
"cdna_end": null,
"cdna_length": 1646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "c.385C>T",
"hgvs_p": "p.Gln129*",
"transcript": "ENST00000637455.1",
"protein_id": "ENSP00000489628.1",
"transcript_support_level": 5,
"aa_start": 129,
"aa_end": null,
"aa_length": 321,
"cds_start": 385,
"cds_end": null,
"cds_length": 966,
"cdna_start": 385,
"cdna_end": null,
"cdna_length": 1512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.*376C>T",
"hgvs_p": null,
"transcript": "ENST00000430521.2",
"protein_id": "ENSP00000388068.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.756C>T",
"hgvs_p": null,
"transcript": "ENST00000461210.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.2468C>T",
"hgvs_p": null,
"transcript": "ENST00000465925.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.3082C>T",
"hgvs_p": null,
"transcript": "ENST00000473163.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.995C>T",
"hgvs_p": null,
"transcript": "ENST00000476226.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.1273C>T",
"hgvs_p": null,
"transcript": "ENST00000476828.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"hgvs_c": "n.1001C>T",
"hgvs_p": null,
"transcript": "ENST00000478594.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
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"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AMT",
"gene_hgnc_id": 473,
"dbsnp": "rs121964986",
"frequency_reference_population": 0.000017102999,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.000017103,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4830000102519989,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.15000000596046448,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.483,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.495,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.15,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000273588.9",
"gene_symbol": "AMT",
"hgnc_id": 473,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Gln192*"
},
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000636166.1",
"gene_symbol": "ENSG00000283189",
"hgnc_id": null,
"effects": [
"stop_gained"
],
"inheritance_mode": "",
"hgvs_c": "c.811C>T",
"hgvs_p": "p.Gln271*"
}
],
"clinvar_disease": "Glycine encephalopathy,Glycine encephalopathy 1,Glycine encephalopathy 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Glycine encephalopathy|Glycine encephalopathy 2|Glycine encephalopathy 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}